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Yorodumi- PDB-8c5v: Chemotaxis core signalling unit from E protein lysed E. coli cells -
+Open data
-Basic information
Entry | Database: PDB / ID: 8c5v | |||||||||||||||||||||
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Title | Chemotaxis core signalling unit from E protein lysed E. coli cells | |||||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Chemotaxis / Signal Transduction | |||||||||||||||||||||
Function / homology | Function and homology information regulation of protein histidine kinase activity / negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum-dependent swimming motility / aerotaxis / regulation of bacterial-type flagellum-dependent cell motility / cell tip / protein histidine kinase activity ...regulation of protein histidine kinase activity / negative regulation of protein modification process / detection of chemical stimulus / methyl accepting chemotaxis protein complex / positive regulation of post-translational protein modification / bacterial-type flagellum-dependent swimming motility / aerotaxis / regulation of bacterial-type flagellum-dependent cell motility / cell tip / protein histidine kinase activity / regulation of chemotaxis / thermotaxis / signal complex assembly / receptor clustering / histidine kinase / phosphorelay sensor kinase activity / phosphorelay signal transduction system / establishment of localization in cell / cell motility / cellular response to amino acid stimulus / chemotaxis / transmembrane signaling receptor activity / protein domain specific binding / signal transduction / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 12 Å | |||||||||||||||||||||
Authors | Cassidy, C.K. / Qin, Z. / Zhang, P. | |||||||||||||||||||||
Funding support | United Kingdom, United States, European Union, 6items
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Citation | Journal: mBio / Year: 2023 Title: Structure of the native chemotaxis core signaling unit from phage E-protein lysed cells. Authors: C Keith Cassidy / Zhuan Qin / Thomas Frosio / Khoosheh Gosink / Zhengyi Yang / Mark S P Sansom / Phillip J Stansfeld / John S Parkinson / Peijun Zhang / Abstract: Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and ...Bacterial chemotaxis is a ubiquitous behavior that enables cell movement toward or away from specific chemicals. It serves as an important model for understanding cell sensory signal transduction and motility. Characterization of the molecular mechanisms underlying chemotaxis is of fundamental interest and requires a high-resolution structural picture of the sensing machinery, the chemosensory array. In this study, we combine cryo-electron tomography and molecular simulation to present the complete structure of the core signaling unit, the basic building block of chemosensory arrays, from . Our results provide new insight into previously poorly-resolved regions of the complex and offer a structural basis for designing new experiments to test mechanistic hypotheses. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c5v.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8c5v.ent.gz | 992.8 KB | Display | PDB format |
PDBx/mmJSON format | 8c5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8c5v_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8c5v_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8c5v_validation.xml.gz | 171 KB | Display | |
Data in CIF | 8c5v_validation.cif.gz | 266.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/8c5v ftp://data.pdbj.org/pub/pdb/validation_reports/c5/8c5v | HTTPS FTP |
-Related structure data
Related structure data | 15641MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 42462.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P07363, histidine kinase #2: Protein | Mass: 14874.573 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P07363, histidine kinase #3: Protein | Mass: 15675.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A964 #4: Protein | Mass: 55562.367 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02942 Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Chemotaxis Core Signalling Unit from E-gene lysed E. coli cells. Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 3000 nm |
Image recording | Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: emClarity / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Resolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5100 / Symmetry type: POINT | ||||||||||||||||||||
EM volume selection | Num. of tomograms: 33 / Num. of volumes extracted: 20000 | ||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |